NERDSS

Structure-Resolved Reaction-Diffusion Simulation Software by Johnson Lab, JHU

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Version Information

• Current Version: 1.2.1

  • This version includes the latest stable features

• Parallel NERDSS

  • A parallelized version of NERDSS is in the mpi branch.

Run a quick trial with our server

Go to the NERDSS server.

Installation

To build NERDSS, you need:

1. A C++ compiler:
   • For macOS, install XCode
   • For Ubuntu, install a compiler through apt
2. GNU Scientific Library (GSL) version 1.0 or higher:
   • For macOS, install via Homebrew
   • For Ubuntu, install via apt
3. To compile using make:
   • Navigate to the main directory
   • Run make serial
   • The executable will be placed in the ./bin directory

Running Simulations

1. Example input files are located in the subdirectories within the sample_inputs folder. They can also be generated using the python GUI program, which is also included in the ioNERDSS tool.

2. To start the simulation, use the command ./nerdss -f parms.inp.

Analyzing Results

1. Use the ioNERDSS PyPi library for visualizing simulation results.
2. Install ioNERDSS with pip install ioNERDSS.
3. Refer to the ionerdss repository for more details.